Getting the obvious bit out of the way: it's about abuse.
The story is narrated by someone outside the relationship. A friend of the abused, perhaps something more.
"You just don't dare.
And inside you're yearning
With some secret burning"
He's calling the abused out a bit here. They want something better, but something's stopping them from leaving.
"Still won't you help me,
I'm flawed, desperate, angry with God,
cause he just won't care,
oh, excuse me, you're mourning,
how callous and boring"
He has things he needs to talk about as well, but he feels like all they talk about are the abused's issues.
"I brush your hair
See your face, empty smile"
They return to the topic of abuse.
"you know it wont stop, so you make an excuse to confuse the issue,
what make you think that i'll care about you?
when you lay on the ground till he tells you he's through"
This is pretty straightforward. He's explaining the situation. The interesting bit is that he asks, "what makes you think that I'll care about you?" And it's a big, important part of the song. He's basically asking why should he care if the abused doesn't seem to care. The abused knows what's going on is terrible, but they lie down and take it. And the narrator claims that he's going to put as little thought into the abuse as they do.
"so it finally dawned on me, yesterday morning,
i just can't stare,
and swallow the words, that your hero's perverted on what we share,
i'll kill him, I'll beat him. The cycle's repeating.
I hold thin arrogance"
We see how much he actually cares about the situation despite his talk. He can't keep pretending that nothing is happening while the abuser is perverting the abused's perspective of the relationship between the narrator and the abused. He makes plans to attack the abuser. Perhaps he does, or maybe the abused tells the abuser of the plan, but it causes more issues in the abusive relationship. He acknowledges that he was arrogant in thinking he could change anything.
"still wont you hold him and trust him,
you love him, so much, and he still wont care,
to see your face, with an empty smile,
cause i touched that place on you, and all the while"
He sees that the abused is planting their feet in their abusive relationship, but her loyalty doesn't matter to the abuser. He states that the abuser will never see the abused in the same way that he does.
"she says it's so good, when it's so good,
this is so good, when it's no good,
this is so good, everybody so good,
everybody so good, when you're no good,
all the while, he's been using you,
yes all the while, he's abusing you"
A common thing happens in abusive relationships where the abused will try to rationalize the relationship. "It's so good when it's so good" is basically saying "sure, he constantly makes me fear for my life, but when he's sweet, he can be sweet".
"with your naked excuse you confuse your misuse,
what makes you think that I should care what he'll do
you lay on the ground till he tells you he's through,
and he makes up your mind that that's what you should do"
He calls the abused out again. And he, again, asks them why he should care if she doesn't care. But he's really trying to talk himself out of his feelings for the abused. He's trying to see the situation for what it is, hopeless.
"cause all the while you, you've been using you,
yes all the while, you've been abusing you,
he hurts you, miss treats you, your own mind misleads you,
you just won't care,
when holes in your face cant be covered with makeup you'll still stay there."
He's more or less saying that the abuse won't stop, and that the violence is only going to get worse. It'll either end with the abuse getting so bad that no one can ignore it and they'll get involved like he did, or until she gets killed.
Tl;dr
It's a song about a man's relationship with a woman in an abusive relationship. He tries to get involved, but makes things worse. And after coming to grips with the fact that she'll never leave, he decides to leave.
Getting the obvious bit out of the way: it's about abuse.
The story is narrated by someone outside the relationship. A friend of the abused, perhaps something more.
"You just don't dare. And inside you're yearning With some secret burning"
He's calling the abused out a bit here. They want something better, but something's stopping them from leaving.
"Still won't you help me, I'm flawed, desperate, angry with God, cause he just won't care, oh, excuse me, you're mourning, how callous and boring"
He has things he needs to talk about as well, but he feels like all they talk about are the abused's issues.
"I brush your hair See your face, empty smile"
They return to the topic of abuse.
"you know it wont stop, so you make an excuse to confuse the issue, what make you think that i'll care about you? when you lay on the ground till he tells you he's through"
This is pretty straightforward. He's explaining the situation. The interesting bit is that he asks, "what makes you think that I'll care about you?" And it's a big, important part of the song. He's basically asking why should he care if the abused doesn't seem to care. The abused knows what's going on is terrible, but they lie down and take it. And the narrator claims that he's going to put as little thought into the abuse as they do.
"so it finally dawned on me, yesterday morning, i just can't stare, and swallow the words, that your hero's perverted on what we share, i'll kill him, I'll beat him. The cycle's repeating. I hold thin arrogance"
We see how much he actually cares about the situation despite his talk. He can't keep pretending that nothing is happening while the abuser is perverting the abused's perspective of the relationship between the narrator and the abused. He makes plans to attack the abuser. Perhaps he does, or maybe the abused tells the abuser of the plan, but it causes more issues in the abusive relationship. He acknowledges that he was arrogant in thinking he could change anything.
"still wont you hold him and trust him, you love him, so much, and he still wont care, to see your face, with an empty smile, cause i touched that place on you, and all the while"
He sees that the abused is planting their feet in their abusive relationship, but her loyalty doesn't matter to the abuser. He states that the abuser will never see the abused in the same way that he does.
"she says it's so good, when it's so good, this is so good, when it's no good, this is so good, everybody so good, everybody so good, when you're no good, all the while, he's been using you, yes all the while, he's abusing you"
A common thing happens in abusive relationships where the abused will try to rationalize the relationship. "It's so good when it's so good" is basically saying "sure, he constantly makes me fear for my life, but when he's sweet, he can be sweet".
"with your naked excuse you confuse your misuse, what makes you think that I should care what he'll do you lay on the ground till he tells you he's through, and he makes up your mind that that's what you should do"
He calls the abused out again. And he, again, asks them why he should care if she doesn't care. But he's really trying to talk himself out of his feelings for the abused. He's trying to see the situation for what it is, hopeless.
"cause all the while you, you've been using you, yes all the while, you've been abusing you, he hurts you, miss treats you, your own mind misleads you, you just won't care, when holes in your face cant be covered with makeup you'll still stay there."
He's more or less saying that the abuse won't stop, and that the violence is only going to get worse. It'll either end with the abuse getting so bad that no one can ignore it and they'll get involved like he did, or until she gets killed.
Tl;dr It's a song about a man's relationship with a woman in an abusive relationship. He tries to get involved, but makes things worse. And after coming to grips with the fact that she'll never leave, he decides to leave.